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- PDB-6v73: Crystal Structure of Metallo Beta Lactamase from Erythrobacter li... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6v73 | ||||||
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Title | Crystal Structure of Metallo Beta Lactamase from Erythrobacter litoralis with beta mercaptoethanol in the active site | ||||||
![]() | Beta-lactamase II | ||||||
![]() | HYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | ![]() antibiotic catabolic process / beta-lactamase / hydrolase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Maltseva, N. / Kim, Y. / Clancy, S. / Endres, M. / Mulligan, R. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal Structure of Metallo Beta Lactamase from Erythrobacter litoralis with beta mercaptoethanol in the active site Authors: Maltseva, N. / Kim, Y. / Clancy, S. / Endres, M. / Mulligan, R. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 122.9 KB | Display | ![]() |
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PDB format | ![]() | 78.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 270.8 KB | Display | ![]() |
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Full document | ![]() | 270.7 KB | Display | |
Data in XML | ![]() | 1.2 KB | Display | |
Data in CIF | ![]() | 3.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6v72S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 25956.982 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) ![]() References: UniProt: Q2N9N3 |
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-Non-polymers , 5 types, 29 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/BME.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/BME.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-BME / | #5: Chemical | ChemComp-FMT / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.73 Å3/Da / Density % sol: 67.06 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 3.5M Sodium formate; 0.1M TRIS pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Dec 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 15857 / % possible obs: 99.6 % / Redundancy: 15.1 % / Biso Wilson estimate: 56.42 Å2 / Rsym value: 0.124 / Net I/σ(I): 24.5 |
Reflection shell | Resolution: 2.4→2.44 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 735 / CC1/2: 0.527 / Rsym value: 1.052 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6V72 Resolution: 2.4→39.65 Å / SU ML: 0.276 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.4066
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.75 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→39.65 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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